Jürgen Cox

Summary

Country: Germany

Publications

  1. doi request reprint A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Protoc 4:698-705. 2009
  2. doi request reprint Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap
    Jürgen Cox
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Am Soc Mass Spectrom 20:1477-85. 2009
  3. doi request reprint Quantitative, high-resolution proteomics for data-driven systems biology
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried D 82152, Germany
    Annu Rev Biochem 80:273-99. 2011
  4. pmc Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
    Jürgen Cox
    From the Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 13:2513-26. 2014
  5. pmc 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
    Juergen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    BMC Bioinformatics 13:S12. 2012
  6. pmc PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    Florian Gnad
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 8:R250. 2007
  7. pmc Software lock mass by two-dimensional minimization of peptide mass errors
    Jürgen Cox
    Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    J Am Soc Mass Spectrom 22:1373-80. 2011
  8. doi request reprint Andromeda: a peptide search engine integrated into the MaxQuant environment
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 10:1794-805. 2011
  9. doi request reprint MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Biotechnol 26:1367-72. 2008
  10. doi request reprint High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 9:4642-52. 2009

Collaborators

Detail Information

Publications40

  1. doi request reprint A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Protoc 4:698-705. 2009
    ..The software is freely available at the MaxQuant home page...
  2. doi request reprint Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap
    Jürgen Cox
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Am Soc Mass Spectrom 20:1477-85. 2009
    ..This extremely high and individualized mass accuracy is equivalent to a substantial increase in database identification score...
  3. doi request reprint Quantitative, high-resolution proteomics for data-driven systems biology
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried D 82152, Germany
    Annu Rev Biochem 80:273-99. 2011
    ..The large-scale nature of proteomics data and its high accuracy pose special opportunities as well as challenges in systems biology that have been largely untapped so far...
  4. pmc Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
    Jürgen Cox
    From the Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 13:2513-26. 2014
    ..It is implemented in the freely available MaxQuant computational proteomics platform and works completely seamlessly at the click of a button. ..
  5. pmc 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
    Juergen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    BMC Bioinformatics 13:S12. 2012
    ..We also describe one-dimensional annotation enrichment, which can be applied to single omics data. The 1D and 2D annotation enrichment algorithms are freely available as part of the Perseus software...
  6. pmc PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    Florian Gnad
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 8:R250. 2007
    ..For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites...
  7. pmc Software lock mass by two-dimensional minimization of peptide mass errors
    Jürgen Cox
    Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    J Am Soc Mass Spectrom 22:1373-80. 2011
    ..maxquant.org )...
  8. doi request reprint Andromeda: a peptide search engine integrated into the MaxQuant environment
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 10:1794-805. 2011
    ..We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides...
  9. doi request reprint MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Biotechnol 26:1367-72. 2008
    ..MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates...
  10. doi request reprint High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 9:4642-52. 2009
    ..We constructed a yeast-specific phosphorylation sites predictor on the basis of a support vector machine, which - together with the yeast phosphorylation data - is integrated into the PHOSIDA database (www.phosida.com)...
  11. doi request reprint Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Jesper V Olsen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried near Munich, Germany
    Sci Signal 3:ra3. 2010
    ..In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells...
  12. pmc An integrated phosphoproteomics work flow reveals extensive network regulation in early lysophosphatidic acid signaling
    Thiemo B Schreiber
    Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 9:1047-62. 2010
    ....
  13. doi request reprint Comparison of SILAC and mTRAQ quantification for phosphoproteomics on a quadrupole orbitrap mass spectrometer
    Felix S Oppermann
    Evotec München GmbH, Am Klopferspitz 19a, 82152 Martinsried, Germany
    J Proteome Res 12:4089-100. 2013
    ..In conclusion, our results demonstrate a strong analytical performance of the Q Exactive in global phosphoproteomics, and establish mTRAQ quantification as a useful alternative to metabolic isotope labeling. ..
  14. doi request reprint High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome
    Nadin Neuhauser
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 12:2858-68. 2013
    ..We apply our high performance platform to investigate incremental coverage of the human proteome by high resolution MS data originating from in-depth cell line and cancer tissue proteome measurements...
  15. pmc Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles
    Sally J Deeb
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:77-89. 2012
    ..These results show that high resolution shotgun proteomics combined with super-SILAC-based quantification is a promising new technology for tumor characterization and classification...
  16. doi request reprint Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes
    Chunaram Choudhary
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Mol Cell 36:326-39. 2009
    ..Thus, intracellular activation of RTKs by oncogenic mutations in the biosynthetic route may exploit cellular architecture to initiate aberrant signaling cascades, thus evading negative regulation...
  17. pmc A framework for intelligent data acquisition and real-time database searching for shotgun proteomics
    Johannes Graumann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.013185. 2012
    ..Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available...
  18. pmc Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response
    Kirti Sharma
    Departments of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.014654. 2012
    ..This study defines the cellular response to Hsp90 inhibition at the proteome level and sheds light on the mechanisms by which it can be used to target cancer cells...
  19. doi request reprint How much peptide sequence information is contained in ion trap tandem mass spectra?
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Am Soc Mass Spectrom 19:1813-20. 2008
    ..Thus, optimal de novo sequencing algorithms should be able to obtain substantial sequence information in at least half of all cases...
  20. doi request reprint Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    Lyris M F de Godoy
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nature 455:1251-4. 2008
    ..Systems-wide, precise quantification directly at the protein level opens up new perspectives in post-genomics and systems biology...
  21. doi request reprint Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling
    Kirti Sharma
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Cell Rep 8:1583-94. 2014
    ..Unexpectedly, it is enriched on higher-abundance proteins, and this correlates with the substrate KM values of tyrosine kinases. Our data suggest that P-Tyr should be considered a functionally separate PTM of eukaryotic proteomes. ..
  22. doi request reprint In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis
    Sara Zanivan
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Cell Rep 3:552-66. 2013
    ..This detailed molecular picture, both at the proteome and phosphoproteome level, will prove useful for the study of mechanisms of tumor progression...
  23. pmc Expert system for computer-assisted annotation of MS/MS spectra
    Nadin Neuhauser
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:1500-9. 2012
    ..biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions...
  24. ncbi request reprint Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins
    Johannes Graumann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 7:672-83. 2008
    ..We compared the proteome with a recently published map of chromatin states of promoters in ES cells and found excellent correlation between protein expression and the presence of active and repressive chromatin marks...
  25. pmc Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions
    Nina C Hubner
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
    J Cell Biol 189:739-54. 2010
    ..The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome...
  26. doi request reprint The coming age of complete, accurate, and ubiquitous proteomes
    Matthias Mann
    Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
    Mol Cell 49:583-90. 2013
    ..Developments discussed in this Perspective will soon enable complete proteome analysis of mammalian cells, as well, with profound impact on biology and biomedicine...
  27. pmc Predicting post-translational lysine acetylation using support vector machines
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Bioinformatics 26:1666-8. 2010
    ..This dataset should provide an excellent source to train support vector machines (SVMs) allowing the high accuracy in silico prediction of acetylated lysine residues...
  28. doi request reprint Combined use of RNAi and quantitative proteomics to study gene function in Drosophila
    Tiziana Bonaldi
    Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell 31:762-72. 2008
    ..We found little overall correlation between changes in the transcriptome and proteome with many protein changes unaccompanied by message changes. However, correlation was high for those mRNAs that changed significantly by microarray...
  29. ncbi request reprint Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry
    Sara Zanivan
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 7:5314-26. 2008
    ..Thus, solid tumor can be analyzed by MS-based proteomics with similar efficiency as cell culture models and in amounts compatible with biopsies...
  30. doi request reprint A systematic investigation into the nature of tryptic HCD spectra
    Annette Michalski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    J Proteome Res 11:5479-91. 2012
    ..Overall, 84% of the fragment ion intensity was unambiguously explainable. Thus high mass accuracy HCD and CID data are near comprehensively and automatically interpretable...
  31. doi request reprint Quantitative proteomics reveals subset-specific viral recognition in dendritic cells
    Christian A Luber
    Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Immunity 32:279-89. 2010
    ....
  32. pmc A "Proteomic Ruler" for Protein Copy Number and Concentration Estimation without Spike-in Standards
    Jacek R Wisniewski
    From the Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 13:3497-506. 2014
    ..The proteomic ruler approach is readily applicable to any deep eukaryotic proteome dataset-even in retrospective analysis-and we demonstrate its usefulness with a series of mouse organ proteomes. ..
  33. pmc In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism
    Maria S Robles
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    PLoS Genet 10:e1004047. 2014
    ..Our large-scale proteomic analysis reveals thus that circadian post-transcriptional and post-translational mechanisms play a key role in the temporal orchestration of liver metabolism and physiology. ..
  34. doi request reprint Proteomics strategy for quantitative protein interaction profiling in cell extracts
    Kirti Sharma
    Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Nat Methods 6:741-4. 2009
    ..We demonstrate the general utility of this methodology in interaction studies involving small-molecule kinase inhibitors, a tyrosine-phosphorylated peptide and an antibody as affinity ligands...
  35. pmc A novel chromatographic method allows on-line reanalysis of the proteome
    Leonie F Waanders
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 7:1452-9. 2008
    ..We demonstrate three principal advantages of this system: nearly continuous MS utilization, duplicate analysis without requirement for additional sample, and targeting of important but undersampled features in the replay run...
  36. doi request reprint Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors
    Atul S Deshmukh
    From the Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 14:841-53. 2015
    ..This revealed unexpectedly complex regulation of AMP-activated protein kinase and insulin signaling in muscle tissue at the level of enzyme isoforms. ..
  37. pmc Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells
    Silvia Stingele
    Group of Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 8:608. 2012
    ..Our data present the first broad proteomic analysis of human cells with abnormal karyotypes and suggest a uniform cellular response to the presence of an extra chromosome...
  38. ncbi request reprint Is proteomics the new genomics?
    Jürgen Cox
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
    Cell 130:395-8. 2007
    ..Is it now ready to tackle comprehensive protein expression analysis?..
  39. doi request reprint MaxQuant for in-depth analysis of large SILAC datasets
    Stefka Tyanova
    Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
    Methods Mol Biol 1188:351-64. 2014
    ..Here we provide a step-by-step protocol explaining how the current MaxQuant version can be used to analyze large SILAC-labeling datasets in an efficient way...
  40. ncbi request reprint Analysis of the mouse liver proteome using advanced mass spectrometry
    Rong Shi
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 6:2963-72. 2007
    ..3%, transmembrane domains were predicted. For potential application in toxicology or clinical studies, we demonstrate that it is possible to consistently identify more than 1000 proteins in a single run...